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. 2015 Sep 21;29(1):36–42. doi: 10.5713/ajas.15.0476

Table 2.

Highly selective SNPs with any p-value <0.001 (top 1% SNPs) in the analysis of milk yield, fat and protein phenotypes and the genes containing it1

Chromosome SNP SNP position MRSC FRSC PRSC Milk2 Fat3 Protein4 GeneID5 Gene start Gene end Gene name
1 ARS-BFGL-NGS-29472 138,650,000 0.444 0.769 0.530 0.013455 0.000053 0.011769 ENSBTAG00000012798 138,455,304 138,676,649 KCNH8
2 ARS-BFGL-NGS-107330 116,829,914 0.653 0.305 0.783 0.000563 0.063954 0.000402 ENSBTAG00000021327 116,803,654 116,839,529 DAW1
3 BTA-99819-no-rs 79,508,402 −0.742 −0.698 −0.842 0.000098 0.000184 0.000142 ENSBTAG00000008636 79,284,893 79,734,224 PDE4B
3 BTB-01155479 79,378,528 −0.754 −0.841 −0.957 0.000078 0.000009 0.000018 ENSBTAG00000008636 79,284,893 79,734,224 PDE4B
3 ARS-BFGL-NGS-31953 79,480,234 −0.757 −0.693 −0.866 0.000073 0.000205 0.000094 ENSBTAG00000008636 79,284,893 79,734,224 PDE4B
3 Hapmap39300-BTA-99855 79,333,053 −0.803 −0.881 −0.994 0.000028 0.000004 0.000009 ENSBTAG00000008636 79,284,893 79,734,224 PDE4B
3 ARS-BFGL-NGS-102149 110,078,547 0.555 0.742 0.672 0.002813 0.000091 0.002019 ENSBTAG00000015969 110,074,348 110,109,946 STK40
3 BTB-01582389 40,625,026 0.570 0.651 0.651 0.002235 0.000524 0.002682 ENSBTAG00000021217 40,448,699 40,682,012 COL11A1
3 ARS-BFGL-NGS-112442 40,588,026 0.577 0.619 0.655 0.002023 0.000920 0.002540 ENSBTAG00000021217 40,448,699 40,682,012 COL11A1
3 ARS-BFGL-NGS-64215 15,525,599 −0.622 −0.759 −0.802 0.000899 0.000054 0.000272 ENSBTAG00000020244 15,521,494 15,528,093 EFNA1
4 BTB-00172204 31,172,819 0.326 0.690 0.524 0.052424 0.000256 0.012614 ENSBTAG00000015539 31,017,033 31,222,267 RAPGEF5
5 Hapmap53993-rs29024740 60,373,086 0.499 0.678 0.567 0.006441 0.000316 0.007694 ENSBTAG00000003183 60,372,425 60,502,966 NTN4
5 BTB-00239812 121,135,969 0.582 0.229 0.723 0.001852 0.127036 0.000990 ENSBTAG00000020341 121,099,143 121,164,873 MOV10L1
6 ARS-BFGL-NGS-4767 107,186,270 0.515 0.806 0.578 0.005127 0.000024 0.006713 ENSBTAG00000005711 106,483,716 107,356,158 NSG1
6 Hapmap38694-BTA-76566 61,591,415 0.533 0.401 0.783 0.003943 0.022142 0.000402 ENSBTAG00000027569 61,362,546 61,744,231 APBB2
9 BTB-00404639 90,037,629 1.000 0.605 0.708 0.000000 0.001172 0.001220 ENSBTAG00000007159 89,969,586 90,255,801 ESR1
9 Hapmap47116-BTA-84683 90,002,616 0.776 0.624 0.514 0.000054 0.000849 0.014135 ENSBTAG00000007159 89,969,586 90,255,801 ESR1
10 ARS-BFGL-NGS-113766 81,459,970 −0.790 0.060 −0.842 0.000037 0.389680 0.000142 ENSBTAG00000009998 81,396,104 81,494,769 GALNTL1
10 ARS-BFGL-NGS-82682 89,774,836 0.698 0.095 0.775 0.000249 0.322371 0.000452 ENSBTAG00000020480 89,756,991 89,852,261 SPTLC2
10 ARS-BFGL-NGS-110578 91,602,885 0.628 0.314 0.771 0.000863 0.058033 0.000483 ENSBTAG00000025324 91,597,994 92,223,876 NRXN3
10 ARS-BFGL-NGS-3900 89,804,719 0.689 0.087 0.759 0.000296 0.337759 0.000583 ENSBTAG00000020480 89,756,991 89,852,261 SPTLC2
11 ARS-BFGL-NGS-51235 37,228,325 0.627 0.368 0.835 0.000889 0.032657 0.000177 ENSBTAG00000006995 37,030,009 37,241,384 SPTBN1
13 ARS-BFGL-NGS-90758 35,352,877 0.201 0.630 0.212 0.159441 0.000762 0.185064 ENSBTAG00000001204 35,331,913 35,368,126 JCAD
13 Hapmap60259-rs29016362 34,887,980 0.067 0.627 0.112 0.373241 0.000804 0.319634 ENSBTAG00000027444 34,860,211 34,965,895 SVIL
13 Hapmap49926-BTA-24453 21,167,068 −0.226 −0.740 −0.349 0.126467 0.000081 0.065057 ENSBTAG00000023216 21,049,546 21,386,152
15 ARS-BFGL-NGS-107160 75,065,222 0.160 0.636 0.418 0.214312 0.000685 0.037164 ENSBTAG00000008465 75,047,569 75,068,534 ACS
17 ARS-BFGL-NGS-11818 4,393,229 0.745 0.449 0.775 0.000100 0.012179 0.000452 ENSBTAG00000008816 4,308,229 4,436,083 TRIM2
17 BTB-00668797 4,827,067 0.707 0.670 0.775 0.000210 0.000371 0.000452 ENSBTAG00000008438 4,732,242 4,868,678 ARFIP1
17 ARS-BFGL-NGS-77442 63,480,469 0.576 0.413 0.759 0.002035 0.019096 0.000576 ENSBTAG00000001806 63,474,993 63,497,850 IQCD
21 ARS-BFGL-NGS-104549 57,731,221 0.689 0.291 0.738 0.000296 0.073074 0.000794 ENSBTAG00000006620 57,596,461 57,783,306 SLC24A4
22 Hapmap38236-BTA-55228 10,502,283 0.624 0.625 0.926 0.000925 0.000826 0.000037 ENSBTAG00000016758 10,492,112 10,585,992 MLH1
23 Hapmap55007-rs29021986 13,484,531 0.361 0.617 0.380 0.036246 0.000945 0.052479 ENSBTAG00000027197 13,389,447 13,520,727 KIF6
25 ARS-BFGL-NGS-93374 17,040,004 0.602 0.654 0.906 0.001351 0.000497 0.000052 ENSBTAG00000016505 17,039,666 17,081,449 TMC7
26 ARS-BFGL-NGS-19663 43,933,332 0.931 0.691 0.919 0.000002 0.000249 0.000041 ENSBTAG00000018941 43,829,293 43,966,907 CPXM2
26 ARS-BFGL-NGS-110497 45,870,133 0.542 0.620 0.604 0.003440 0.000895 0.004904 ENSBTAG00000012444 45,848,827 46,238,138 ADAM12
26 ARS-BFGL-NGS-30392 44,539,739 −0.526 −0.750 −0.464 0.004132 0.000065 0.022510 ENSBTAG00000010957 44,431,214 44,558,731 LHPP
26 ARS-BFGL-NGS-30060 45,983,109 0.673 0.606 0.805 0.000394 0.001141 0.000282 ENSBTAG00000012444 45,848,827 46,238,138 ADAM12
28 ARS-BFGL-NGS-28818 7,138,132 0.378 0.614 0.318 0.030058 0.000997 0.087874 ENSBTAG00000020361 6,762,322 7,195,661 SLC35F3

SNP, single nucleotide polymorphism; MRSC, milkyield relative selection coefficient; FRSC, fat relative selection coefficient; PRSC, protein relative selection coefficient.

1

p-value was computed under the normality assumption of relative selection coefficient. The gene catalog was retrieved from Ensembl server.

2

Milkyield p-value.

3

Fat p-value.

4

Protein p-value.

5

Ensembl gene ID.